Is CABP4 p.Ala23Val (c.68C>T) pathogenic?

CABP4 p.Ala23Val (c.68C>T) is classified Likely benign in CABP4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-29). AlphaMissense: likely benign (0.0764); Rare (popmax 0.107%, amr); Associated with Inborn genetic diseases.

What condition is associated with CABP4 p.Ala23Val (c.68C>T)?

CABP4 p.Ala23Val (c.68C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CABP4 p.Ala23Val (c.68C>T) in the general population?

CABP4 p.Ala23Val (c.68C>T) is rare (popmax 0.107%, amr) (gnomAD).

What do computational predictors say about CABP4 p.Ala23Val (c.68C>T)?

AlphaMissense predicts likely benign (score 0.0764) — an in-silico prediction, not a clinical call.

CABP4 p.Ala23Val

c.68C>T · rs371921931 · VCV1561026

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0764 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.107%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0764	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -7.25	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.4	GERP -3.6
Regional constraint	o/e 1.07	unconstrained · MANE · 3,232 bp · p 0.15 · regional, not allelic
Overall
CADD	0.184	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.107% Admixed American · 63/58,944 alleles

Filtering AF 0.0856% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.078%

Overall 0.00628% 101/1,607,940 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.107%	936
Middle Eastern	0.0332%	3,009
Remaining individualsnot grpmax-eligible	0.00482%	20,749
European (non-Finnish)	0.00255%	39,273
South Asian	0.00222%	45,044
Finnishnot grpmax-eligible	0.0016%	62,528

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CABP4
Protein: p.Ala23Val
Coding: c.68C>T
MANE Select: NM_145200
dbSNP: rs371921931
Type: single nucleotide variant
Location: chr11:67455491 (GRCh38)
Gene constraint: LOEUF 1.345 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 65.01
Residue 23: the 'disordered' region

Full CABP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CABP4 p.Ala23= Conflicting classifications of pathogenicity ★ same residue
CABP4 p.Ala23Gly Uncertain significance ★ ⚠ same residue
CABP4 p.Ala107Thr Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala108Thr Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala137Thr Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala203Val Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala229Val Uncertain significance ★★ ⚠ same condition
CABP4 p.Ala234Val Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cabp4-p-ala23val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown